Uncovering the interplay between regulatory regions and gene coding regions is essential for understanding the mechanisms governing gene regulation in health and disease. Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) offers a new strategy for mapping chromatin interaction networks on a global scale with high resolution and specificity. Data generated from ChIA-PET analysis can be used to map protein-factor binding sites, as well as to construct genome-wide chromatin interactome maps associated with a specific protein factor of interest. The proposed Workshop on Chromatin Interaction Analysis by Paired End- Tag Sequencing, will train young scientists (graduate students, post-doctoral trainees, new investigators) in the use of ChIA-PET as a tool for asking questions about chromatin interactions, 3D genome organization and genome regulation in human health and disease. Our five-day ChIA-PET workshop provides a balance of didactic and laboratory-based instruction with ample opportunities for interactions among participants and course faculty. Participants will conduct a ChIA-PET experiment from the chromatin immunoprecipitation (ChIP) step to high throughput sequencing and through the bioinformatics analysis and data processing phases. In 2014 JAX successfully piloted the ChIA-PET workshop and a registration waitlist demonstrated significant demand for this technical training. The 4D Nucleome project initiated by the NIH Common Fund in 2015 will further increase research activity within this field and will likely generate significant additional interet in ChIA-PET and related technologies. The proposed course will be held annually during the late fall at The Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. Lectures, discussions, and laboratory work will be held morning, afternoon, and evening for a total of approximately 50 hours of didactic and hands-on training. The Jackson Laboratory is an NCI-designated Basic Research Cancer Center and has a long history of hosting advanced courses and workshops.